SystemError: initialization of rdchem raised unreported exception

[clefourrier]

Hi,
I'm using Python 3.8.10, and trying to import rdchem using from rdkit.Chem import rdchem, with rdkit 2022.9.1, on Ubuntu 20.04.5.

It fails with SystemError: initialization of rdchem raised unreported exception and no other indication.
The command python -c "from rdkit import Chem; print(Chem.MolToMolBlock(Chem.MolFromSmiles('C1CCC1')))", on the other hand, works fine.

[kuelumbus]

Hi, I can't repo this on my Ubuntu or Debian machine. It works fine. Can you tell me a bit more about your environment and system configuration? Do you work in a conda environment? Do you work on an HPC system? What numpy version are you using?

Maybe related: https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg09794.html and rdkit/conda-rdkit#57

[clefourrier]

Env: I'm on a Dell Precision 5560, running under Ubuntu 20.04.5.
I'm launching this from a venv, that I manage with pip (so no conda).
My numpy version is 1.23.0. Edit: going back to numpy 1.12 would break all the other depencies I need for my config.

I initially noticed the problem by trying to import packages from ogb, which depends on rdkit.

I managed to get slightly more detail:

SystemError                               Traceback (most recent call last)
----> 1 from rdkit.Chem import rdchem

File venv/python3.8/site-packages/rdkit/Chem/__init__.py:20, in <module>
     18 from rdkit import DataStructs
     19 from rdkit.Geometry import rdGeometry
---> 20 from rdkit.Chem import rdchem
     21 _HasSubstructMatchStr = rdchem._HasSubstructMatchStr
     22 from rdkit.Chem.rdchem import *

SystemError: initialization of rdchem raised unreported exception

[clefourrier]

Edit: must be a problem from my config somewhere, closing

[kuelumbus]

Ok. Let me know if you need further help.

[clefourrier]

So, for further archive, removing the shebang #!/bin/python3 which started my file solved it (no idea why).